Quantitative Susceptibility Mapping Of Articular Cartilage: Ex Vivo Findings At Multiple Orientations And Following Different Degradation Treatments

This dataset contains all the raw source data and MATLAB analysis functions that comprise the study: <br> Quantitative susceptibility mapping of articular cartilage: Ex vivo findings at multiple orientations and following different degradation treatments Magnetic Resonance in Medicine | DOI: 10.1002/mrm.27216 Nykänen Olli(1*), Rieppo Lassi(2,3), Töyräs Juha(1,4), Kolehmainen Ville(1), Saarakkala Simo(2,3,5), Shmueli Karin(6) and Nissi Mikko Johannes(1) (1) Department of Applied Physics, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland<br> (2) Research Unit of Medical Imaging, Physics and Technology, University of Oulu, POB 5000, FI-90014 Oulu, Finland<br> (3) Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland<br> (4) Diagnostic Imaging Center, Kuopio University Hospital, Kuopio, Finland<br> (5) Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland<br> (6) Department of Medical Physics &amp; Biomedical Engineering, University College London(UCL), London, United Kingdom <br> *Corresponding author:<br> Olli Nykänen<br> Department of Applied Physics,<br> University of Eastern Finland<br> POB 1627<br> FI-70211, Kuopio, Finland<br> [e-mail]<br> [phone] <br> Keywords: cartilage, collagen matrix, quantitative susceptibility mapping, MRI, osteoarthritis <br> Included folders and files are:<br> - article_figures: all figures published in the manuscript<br> - data: all MRI, histological, and PLM data used in this article<br> - matlab_functions: matlab functions used in data analysis with subfolders:<br> - aedes_plugins: plugins for aedes (http://aedes.uef.fi) for calculation of QS- and T2* maps<br> - fitting_functions: functions for fitting relaxation times or TKD-method for QSM, used by the functions in above folder<br> - miscellaneous_functions: small helper functions for a number of small tasks utilized by the other scripts and functions<br> - ReadMe.txt: this file <br> Notes for setting up Aedes correctly for this dataset:<br> Run Aedes -&gt; Tools -&gt; Edit VNMR Defaults:<br> - Return: FT + K-space<br> - DC: off<br> - Zeropadding: off<br> - Sorting &amp; fastread: on<br> - Precision: single<br> - Read_fcn: readvnmr<br> - Orient: no See more info in separate readme files included in each folder. <br> (Olli Nykänen, Apr 17, 2018)